Proteome Discoverer 1.4/2.0/2.1/ and 2.2(!!) Videos

This is the complete list of videos for Thermo Scientific's Proteome Discoverer version compiled by me and some others over the years. As always, please watch all videos in HD for best resolution. Sorry about the sound and my squeaky voice.PROTEOME DISCOVERER 1.4

21. How to extract only proteins with a specific post-translational modification: https://vimeo.com/131230075
22. How to process global peptide and global prosphoproteomics data together into one single report: https://vimeo.com/137643323

13 comments:

I have question regarding Label free quan experiments (PIAD): https://vimeo.com/62280924. You have selected precurssor ion detector in the quantification experiment. However there is one more option which precursor ion quantifier. Can you please share your thoughts on this?

Hey Ben, Few more questions on label free quan using PD 1.4. If i have lets say 4 technical replicates of my sample, so after uploading the raw files in a workflow template. Whether the PD will merge my tech replicate and will give combined result of that particular sample? and the other question is, is it possible to do LFQ of several case control pairs with replicates at a time on PD 1.4

Mark, Thanks! I'm glad you find this useful. I should have exactly that method floating around here somewhere from my postdoc. Can you send me a request to orsburn@vt.edu so I have a reminder and your email address? I'll try and get it to you in the next day or so.

Hi, Absolutely! If you have the quan version of PD, everything from 1.1 (I think...defnitely 1.2) can do labeled quantification. But, unless there is a definite reason you have to stay on PD 1.3, the upgrade to PD 1.4, in most cases, is free. And it is substantially better.

I have used "area detector" node to perform label-free quantification on PD 1.4. I noticed that protein areas may change depending on the manner I deal with my data. Working with triplicates I can select the three .raw files and perform only one search, however, it is possible to search them separately and open a unique report sheet merging the three independent runs. I am wondering what's the best way to do that, could you give an advice?

Hi Ben,Thank you for put together all these tools are very useful. I am quite new at iTRAQ proteomics and I'm using PD1.4. I have been struggling fpr a while dealing with missing quan values. I am comparing a control group (3 tags) and a diseased one (4 tags) (one tag for a master pool), and we are very interested in the proteins that are exclusively expressed for the diseased group, but the ratios of these proteins are not reported as you can suppose. Could you recommend a strategy to find this specific group of proteins? Any help is greatly appreciated.Diana

Hey Ben,It looks like the PD 2.2 video links are not working. Just letting you know and hope you can get them back up soon. I'm looking into PD 2.2 LFQ stuff and was just about to watch those videos :)

thank you for the dissemination of information in the field of proteomics.I watched your videos regarding the use of different versions of proteome discoverer related to SILAC (1.4 and 2.0).I have version 2.2 and some noode that you have in other versions of proteome discoverer are not exactly the same in 2.2. Do you have any advices to build a SILAC WORFLOW: labeled versus unlabeled and the relevant parameters to use ?